Following his transfer to the Archdiocese of Madrid, Cañizares taught catecheticaltheology at the University of Salamanca and fundamental theology at the Conciliar Seminary of Madrid. He later became the director and a professor of the Institute of Religious Science and Catechesis in Madrid, and sat on several commissions and secretariats of the Spanish Episcopal Conference as well. From 1985 to 1992, Cañizares served as director of the Secretariat of the Episcopal Commission for the Doctrine of the Faith. He also founded and was the first president of Asociación Española de Catequistas, and was Director of the review Teología y Catequesis.

He has been a member of Real Academia de la Historia de España since November 2007. Cañizares is sometimes known by his nickname of "Little Ratzinger,"[2] referring to the similar beliefs and opinions between him and Benedict XVI, born Joseph Ratzinger, who himself is aware of and "very amused by this expression."[3]

In 2013 it was reported that the Congregation is preparing a booklet to help priests celebrate the Mass properly and the faithful to participate better. Cardinal Canizares Llovera confirmed this at an address at the Spanish Embassy to the Holy See on "Catholic Liturgy since Vatican II: Continuity and Evolution." "We are preparing it; it will help to celebrate well and to participate well. During his talk the cardinal reiterated the importance Vatican II gave to the liturgy, "whose renewal must be understood in continuity with the Tradition of the Church and not as a break or discontinuity." A break either because of innovations that do not respect continuity or because of an immobility that freezes everything at Pius XII, he said.[4]

In response to an interview in December 2008 Cardinal Cañizares Llovera stated regarding the best way to receive the Eucharist: "What does it mean to receive communion in the mouth? What does it mean to kneel before the Most Holy Sacrament? What does it mean to kneel during the consecration at Mass? It means adoration, it means recognizing the real presence of Jesus Christ in the Eucharist; it means respect and an attitude of faith of a man who prostrates before God because he knows that everything comes from Him, and we feel speechless, dumbfounded, before the wondrousness, his goodness, and his mercy. That is why it is not the same to place the hand, and to receive communion in any fashion, than doing it in a respectful way; it is not the same to receive communion kneeling or standing up, because all these signs indicate a profound meaning."

In August 2010, the Cardinal stated that, due to the impact of earlier cultural impact and formation in children who learn at an earlier age, who are faced with mature issues earlier, and who are enormously influenced by modern morality, ethical systems, and the mass communications media, it might be preferable to start preparations for receiving the Sacraments of Penance and the Eucharist at an earlier age, which could also lead to lowering the age of reception for those sacraments (which is now about 7 or 8, the age of reason, where young children begin to be held responsible for their actions and belief systems).

In regard to the motu proprioSummorum Pontificum, Cañizares Llovera has stated, "[The] intention of the Pope has not only been to satisfy the followers ofMonsignor Lefevbre, nor to confine himself to respond to the just wishes of the faithful who feel attached...to the liturgical heritage represented by the Roman Rite, but also, and in a special way, to open the liturgical richness of the Church to all the faithful, thus making possible the discovery of the treasures of the liturgical patrimony of the Church to those who still do not know it...even if there were not a single 'traditionalist' whom to satisfy, this 'discovery' would have been enough to justify the provisions of the Pope."

Speaking in the context of an abortion debate prompted by a Spanish government proposal, the Cardinal said: “What happened in some schools cannot be compared with the millions of lives that have been destroyed by abortion. It has legally destroyed 40 million human lives.” [6]